How to get publications associated with list of genes

Question: How to get publications associated with list of genes

5 months ago by

raya.girish • 20 wrote:

Hi ,

I have list of genes with information whether the genes is deleted or duplicated. I want to know is there any easiest way where i can paste the list of genes and key words like "autism" and i get all the related publication in which autism related genes (my gene list) are highlighted with evidence.

publication mining text mining • 326 views

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modified 3 months ago by Maria_Levchenko • 70 • written 5 months ago by raya.girish • 20

I suggest you start looking into NCBI eUtils as one option to search pubmed database.

ADD REPLY • link written 5 months ago by genomax ♦ 59k

see

ADD REPLY • link written 5 months ago by Pierre Lindenbaum ♦ 115k

@Pierre: OP is asking about how to get publications associated with a list of genes.

ADD REPLY • link written 5 months ago by genomax ♦ 59k

3 months ago by

Maria_Levchenko • 70

EMBL-EBI

Maria_Levchenko • 70 wrote:

Europe PMC Annotations API can be useful: https://europepmc.org/AnnotationsApi. It is based on public text-mining data provided by the research community and made available by Europe PMC programmatically.

In your case you can retrieve all text-mined annotations (including gene names) for a list of publications that have an entity of interest (in your example the entity would be autism). To do this use Annotations by Entity module, input (autism) as an entity, and set the filter parameter to 0. Filter parameter allows you to retrieve all annotation types for the list of articles that contain your specific entity (e.g. autism). Once you have retrieved a full list of annotations you can simply filter them to get only gene/protein type annotations. Here is an example with JSON output: https://www.ebi.ac.uk/europepmc/annotations_api/annotationsByEntity?entity=autism&filter=1&format=JSON&pageSize=4.

If you have a combination of keywords (e.g. autism AND children) you can first use the search module of the Articles API (https://europepmc.org/RestfulWebService#!/Europe32PMC32Articles32RESTful32API/search) with resultType set to idlist. This will retrieve a list of PMIDs that can be pluged in the Annotations API to retrieve all gene mentions from a list of publications (see annotationsByArticleIds).

Disclaimer: I work for Europe PMC.

ADD COMMENT • link written 3 months ago by Maria_Levchenko • 70

5 months ago by

h.mon ♦ 21k

Brazil

h.mon ♦ 21k wrote:

There is a NCBI how-to about this:

How to: Find published information on a gene or sequence

ADD COMMENT • link written 5 months ago by h.mon ♦ 21k

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